A prober working for the Securities and Exchange Commission warned her bosses in 2004 that Bernie Madoff’s financial firm should be investigated for irregularities — but was later told by her superiors to focus on unrelated matters, it was reported today.

Genevievette Walker-Lightfoot, a lawyer for the SEC based in the agency’s Washington office, sent a series of e-mails to one of her bosses, saying that information provided by Madoff during her review didn’t add up, according to documents obtained by The Washington Post.

But Mark Donohue, who worked as a branch chief in Walker-Lightfoot’s department, and his boss Eric Swanson, who later married Madoff’s niece, told her to move on after she alerted them to the money manager’s investments.

In one e-mail, Walker-Lightfoot wrote that not all of Madoff’s transactions “make sense.”

The feds have said that Madoff never actually traded any stocks.

Several of the red flags she tried to bring to her bosses’ attention turned out to be directly related to the $65 billion Ponzi scheme that unraveled this past December amid the faltering economy, the newspaper reported.

The embattled federal agency, however, was under pressure to look for wrongdoing in the mutual fund industry and as a result was unable to pursue the Madoff allegations, officials said.

Madoff eventually confessed to running a giant Ponzi scheme and pleaded guilty to an array of charges — including mail and wire fraud — earlier this year.

On Monday, a federal judge in Manhattan sentenced Madoff, 71, to 150 years behind bars.

Not nailing Madoff for his crimes was a huge embarrassment for the SEC, with the revelation that an employee had tried to launch an investigation further hurting the agency’s credibility as a financial regulatory overseer.

The SEC also was receiving tips about Madoff from Harry Markopolos, who waged a long battle to uncover fraud at Madoff’s company. Markopolos began sounding an alarm in 1999 and continuing with his warnings through this decade.

The feds never acted on the tip and investors lost billions.

The SEC has said that Swanson, one of Walker-Lightfoot’s supervisors, worked on reviews related to Madoff in 1999 and 2004, but never when he was involved with Shana Madoff, whom he married in 2007.

The relationship is currently under investigation by the agency’s inspector general.

Swanson, who no longer works with the agency, also refused comment whan asked by The Washington Post.

Donohue, who still works for the SEC, refused to comment on the report.

The newspaper reported that Walker-Lightfoot left the SEC three years ago after filing a complaint with the agency that she was “subjected to a hostile workplace.”

An SEC investigation of Madoff in 2005 found three violations of minor rules, but no proof of any fraud.